palmer-penguins-pca
JJayes
15/04/2021
Palmer penguins PCA
Reading in data
Penguins data…
## # A tibble: 344 x 8
## species island bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
## <fct> <fct> <dbl> <dbl> <int> <int>
## 1 Adelie Torgersen 39.1 18.7 181 3750
## 2 Adelie Torgersen 39.5 17.4 186 3800
## 3 Adelie Torgersen 40.3 18 195 3250
## 4 Adelie Torgersen NA NA NA NA
## 5 Adelie Torgersen 36.7 19.3 193 3450
## 6 Adelie Torgersen 39.3 20.6 190 3650
## 7 Adelie Torgersen 38.9 17.8 181 3625
## 8 Adelie Torgersen 39.2 19.6 195 4675
## 9 Adelie Torgersen 34.1 18.1 193 3475
## 10 Adelie Torgersen 42 20.2 190 4250
## # ... with 334 more rows, and 2 more variables: sex <fct>, year <int>How do they differ?
Data processing
PCA recipe
Apply the PCA
## # A tibble: 333 x 6
## species PC1 PC2 PC3 PC4 PC5
## <fct> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 Adelie -1.82 -0.596 0.965 0.322 -0.879
## 2 Adelie -1.37 0.313 0.456 0.228 -0.707
## 3 Adelie -1.43 0.115 0.192 0.114 -0.838
## 4 Adelie -1.93 -0.0408 0.813 -0.247 -0.462
## 5 Adelie -1.89 -1.22 1.09 -0.279 -0.693
## 6 Adelie -1.82 0.258 0.415 0.181 -0.743
## 7 Adelie -0.797 -1.02 1.64 -0.229 -0.351
## 8 Adelie -1.85 0.199 -0.0902 0.290 -1.04
## 9 Adelie -1.92 -1.38 1.31 -0.486 -0.537
## 10 Adelie -1.53 -1.11 2.19 -0.545 -0.0420
## # ... with 323 more rowsThis is what the output looks like
What are the components made of?
Plotting the different components
Easy to separate the Gentoos. More difficult to seperate the Adelie and Chinstrap
Using PCA1 and PCA3 it is easy to seperate the different species.
3D plot
We can even make a nice plot in 3-dimensions. You can zoom in and look around with your mouse.